Hi

I want to detect C-terminals and N-terminals in a set of protein PDB files. The loop structure (with no helical/sheet secondary structure) at start of the structure can be counted as N-terminal and similarly the loop region at end for C-terminal. But the problem is that these loops are not always terminus but can be a loop section connecting the protein to another domain which has been chopped off in the PDB. or they can be a extension of a alpha- helices.

Using the protein PDB files how can I detect if these loops (at start/end) are actual terminals?

Thank you in advance